change stageInMode to copy and update module #25
Workflow file for this run
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| name: Run GPU nf-tests | |
| on: | |
| push: | |
| branches: | |
| # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging | |
| - "renovate/**" # branches Renovate creates | |
| pull_request: | |
| branches: [master] | |
| paths: | |
| - ".github/workflows/gpu-tests.yml" | |
| - "modules/nf-core/parabricks/**" | |
| merge_group: | |
| types: [checks_requested] | |
| branches: [master] | |
| workflow_dispatch: | |
| inputs: | |
| runners: | |
| description: "Runners to test on" | |
| type: choice | |
| options: | |
| - "ubuntu-latest" | |
| - "self-hosted" | |
| default: "self-hosted" | |
| # Cancel if a newer run is started | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver | |
| NFTEST_VERSION: "0.9.2" | |
| NXF_ANSI_LOG: false | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver | |
| NXF_VERSION: "24.10.1" | |
| jobs: | |
| nf-test-gpu: | |
| runs-on: "gpu" | |
| name: "GPU | ${{ matrix.tags}} | ${{ matrix.profile }} | ${{ matrix.shard }}" | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| shard: [1, 2] | |
| profile: [docker_self_hosted, singularity] # conda? | |
| # TODO Pass these in from GitHub PR trigger events | |
| tags: | |
| - parabricks/applybqsr | |
| - parabricks/fq2bam | |
| - parabricks/fq2bammeth | |
| env: | |
| NXF_ANSI_LOG: false | |
| TOTAL_SHARDS: 2 | |
| steps: | |
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Run nf-test Action | |
| uses: ./.github/actions/nf-test-action | |
| env: | |
| SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }} | |
| SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }} | |
| SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }} | |
| SENTIEON_AUTH_MECH: "GitHub Actions - token" | |
| with: | |
| profile: ${{ matrix.profile }},gpu | |
| shard: ${{ matrix.shard }} | |
| total_shards: ${{ env.TOTAL_SHARDS }} | |
| tags: ${{matrix.tags}},gpu |